Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13); alanine racemase (EC 5.1.1.1); glutamate racemase (EC 5.1.1.3) (characterized)
to candidate WP_013011779.1 DACET_RS12695 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q9X0Z7 (379 letters) >NCBI__GCF_000025725.1:WP_013011779.1 Length = 428 Score = 172 bits (437), Expect = 1e-47 Identities = 126/411 (30%), Positives = 200/411 (48%), Gaps = 60/411 (14%) Query: 23 PIFETTNFYFDSFDEMSKALRNGDYEFVYKRGSNPTTRLVEKKLAALEECEDARLVASGM 82 PI++TT++ F S + + ++ +Y R NPT ++EK+LA LE A ++SG Sbjct: 24 PIYQTTSYVFKSSEHAANLFGLKEFGNIYSRIMNPTNDVLEKRLADLEGGTGALSLSSGQ 83 Query: 83 SAISLSILHFLSSGDHVVCVDEAYSWAKKFFNYLSKKFDIEVSYVP-PDAERIVEAITKK 141 +AI+ S+L+ ++G ++V Y F Y + IEV +V D E ++A + Sbjct: 84 AAITFSVLNITAAGQNIVASSSIYGGTYNLFKYTLGRLGIEVRFVDGTDPESFIKAADEN 143 Query: 142 TKLIYLESPTSMRMKVIDIRKVTEAAGELKIKTVIDNTWASPIFQKPKLLGVDVVVHSAT 201 T+ Y ES + ++ DIR +++ A E I ++DNT +P KP G D+VV+S T Sbjct: 144 TRAFYTESIGNPAGRLADIRGISDLAHEAGIPLIVDNT-ITPYIFKPFDHGADIVVYSLT 202 Query: 202 KYISGHGDVMAGVI--AGDVEDMKNIF--------------------------------- 226 K+ISG+G + G + GD + Sbjct: 203 KFISGNGTSIGGAVIEKGDFNWANGRYPEITEPDPSYHGLSYWDAFGNHDKAVLRGASYI 262 Query: 227 ----VDEYKNIGPVLSPIEAWLILRGLRTLELRMKKHYENALVVSDFLMDHPKVLEVNYP 282 V +++G LSP A IL GL TL LR+KKH EN+L V++FL HPKV VNY Sbjct: 263 LKARVQLLRDLGSCLSPYSANQILLGLETLPLRIKKHCENSLTVAEFLAKHPKVSWVNYA 322 Query: 283 MNPRSPQYELASSQMSGGSG-LMSFRLKTDSAEKVKEFVESLRVFRMAVSWGSHENLVV- 340 P ++ AS + G G ++ F +K E K+F+ES++VF + G +LV+ Sbjct: 323 GLSDHPDHKKASEILKHGYGAIIGFGIK-GGLESGKKFIESVKVFSHLANVGDARSLVIH 381 Query: 341 ------------PRVAYGDCPKKDVNLIRIHVGLGDPEKLVEDLDQALKKI 379 R++ G + +R+ VG+ D L+ DL+QAL++I Sbjct: 382 PASTTHQQLTTEERISAGVTD----DYVRLSVGIEDVSDLIADLEQALEQI 428 Lambda K H 0.318 0.136 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 379 Number of extensions: 18 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 379 Length of database: 428 Length adjustment: 31 Effective length of query: 348 Effective length of database: 397 Effective search space: 138156 Effective search space used: 138156 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory